Article
Marine & Freshwater Biology
Soraia Vieira, Kasia Sroczynska, Joana Neves, Marta Martins, Maria Helena Costa, Helena Adao, Claudia S. L. Vicente
Summary: This study aimed to understand the spatial distribution patterns and diversity of benthic bacterial communities and nematode assemblages in intertidal sediments in Sado Estuary, Portugal. The results showed significant diversity in bacterial and nematode communities between sampling sites, which was primarily associated with environmental variables such as organic matter and gravel content. The spatial distribution of bacterial communities was more consistent with the ecological conditions of the selected sites at a larger scale, while nematode assemblages exhibited differentiation at the sampling site level, suggesting that their response is influenced by specific factors at a smaller scale. This study provides a fundamental basis for future research on the functional interactions between bacteria and nematodes.
ESTUARINE COASTAL AND SHELF SCIENCE
(2023)
Article
Microbiology
Julia Moll, Friederike Roy, Claus Baessler, Jacob Heilmann-Clausen, Martin Hofrichter, Harald Kellner, Doris Krabel, Jan Henrik Schmidt, Francois Buscot, Bjorn Hoppe
Summary: Nematodes are a diverse and widespread group of organisms in terrestrial environments, with communities in decaying wood influenced by tree species and wood properties, while their diversity is significantly related to the presence of fungi and bacteria.
Article
Environmental Sciences
Hidetoshi Urakawa, Michael A. Kratz, Taylor L. Hancock, Rick A. Armstrong
Summary: This study developed a new method (QT-AMP) for the identification and quantification of Enterococcus using a high-throughput sequencing platform. The method detected 11 Enterococcus species, including three rare species and eight commonly found species, in water samples from three rivers in southwest Florida. QT-AMP showed a higher detection level compared to regular sequencing methods.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Plant Sciences
Ida Romano, Natacha Bodenhausen, Gottlieb Basch, Miguel Soares, Hanna Faist, Friederike Trognitz, Angela Sessitsch, Marce Doubell, Stephane Declerck, Sarah Symanczik
Summary: This study evaluated the impact of different management practices on winter wheat and found that factors such as irrigation, fertilization, and tillage affected wheat yield and microbial activity, as well as rhizosphere- and root-associated microbial communities. The findings help to understand the effects of agricultural practices on microbial communities and provide better monitoring methods for the sustainability of agroecosystems.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Soil Science
Solomon Oloruntoba Samuel, Kazuki Suzuki, Rasit Asiloglu, Naoki Harada
Summary: This study aims to investigate the effects of soil as a microbial source on the assemblage of the endophytic bacterial communities in rice roots. The results showed that the bacterial community in the soils added as a microbial source differed among the soil types, which affected the bacterial community in the hydroponic solution and consequently reflected in the endophytic bacterial community assemblage. Bacterial diversity and richness differed significantly with respect to the microbial sources.
BIOLOGY AND FERTILITY OF SOILS
(2023)
Article
Soil Science
Masanori Kawanobe, Koki Toyota, Karl Ritz
Summary: This study developed highly sensitive primer sets targeting the 18S rDNA region for soil nematode fauna using NGS technology. The NGS analysis of soil DNA with these primer sets showed a higher diversity and more nematode species detection compared to traditional morphological methods. The results indicate that the developed primer sets and metabarcoding protocol are suitable for comprehensive studies of nematode community structure.
APPLIED SOIL ECOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Marcel Suleiman, Francesca Demaria, Cristina Zimmardi, Boris Alexander Kolvenbach, Philippe Francois-Xavier Corvini
Summary: Pharmaceuticals accumulation in the environment is a concern for our planet and health. Little is known about the biodegradation capacity of microbial communities for multiple micropollutants. This study demonstrates the feasibility of cultivating stable microbial communities capable of degrading a mixture of highly concentrated pharmaceuticals.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Ecology
Julio Cesar Garcia-Sanchez, Jose Arredondo-Centeno, Maria Guadalupe Segovia-Ramirez, Ariadna Marcela Tenorio Olvera, Gabriela Parra-Olea, Vance T. Vredenburg, Sean M. Rovito
Summary: Factors such as host phylogeny and climate influence the composition of microbial communities on amphibian skin. The composition of bacterial communities is correlated with host phylogeny, while fungal communities are associated with temperature seasonality and precipitation. Co-occurrence networks of bacteria and fungi show differences in connectivity and negative associations. Including fungi in future studies can provide insights into functional interactions within the microbiome.
Article
Microbiology
Shu Li, Bao Qi, Wan Wang, Xueyan Peng, Andrey A. Gontcharov, Bao Liu, Qi Wang, Yu Li
Summary: The study identified the bacterial communities associated with the plasmodia of six myxomycetes species and found that while the bacterial composition varied among species, there was a high similarity in the functional composition of the bacterial communities. The enrichment for gram-negative and aerobic bacteria in plasmodia suggests that myxomycetes may selectively recruit certain bacteria from the environment.
Article
Microbiology
Peeter Laas, Kelly Ugarelli, Rafael Travieso, Sandro Stumpf, Evelyn E. Gaiser, John S. Kominoski, Ulrich Stingl
Summary: Planktonic microbial communities in wetland ecosystems play a vital role, yet they are relatively underexplored compared to other aquatic ecosystems. This study conducted a high-resolution analysis of bacterial and eukaryotic microbial communities in the Florida Everglades, revealing significant variations along the salinity gradient.
Article
Microbiology
Indira J. Quintero, Anakena M. Castillo, Luis C. Mejia
Summary: This study compared the bacterial communities in soil of two mangrove forest sites in the Panama Bay and found that the community was more diverse in the rural mangrove forest. The dominant phyla of bacteria shared between the two sites were Proteobacteria, Desulfobacterota, and Chloroflexi. The relative abundance of certain bacterial genera increased in the transition from dry to rainy season in the urban mangrove forest.
Article
Soil Science
Antje Bettermann, Jeroen H. T. Zethof, Doreen Babin, Erik L. H. Cammeraat, Albert Sole-Benet, Roberto Lazaro, Lourdes Luna, Joseph Nesme, Soren J. Sorensen, Karsten Kalbitz, Kornelia Smalla, Cordula Vogel
Summary: In this study, the effects of different plant species on microbes, EPS production, and soil aggregation were investigated in two sites in southern Spain. It was found that plant species and site influenced the microbial communities in the rhizoplane, with site being the most important factor. Higher carbonate content in soil reduced the plant-specific effects on microbial communities and subsequent soil aggregation. This study highlights the importance of plant-microbe interactions in soil ecosystem dynamics and the role of soil properties in moderating these interactions.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Environmental Sciences
Mei Wang, Jing Wu, Tong Zhou, Yi Liang, Lixuan Zheng, Yongxue Sun
Summary: The addition of copper and florfenicol significantly impacted denitrification and related gene abundance in agricultural soils, suggesting a potential risk for the spread of drug resistance genes through nitrogen transformation in agricultural soils.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Engineering, Environmental
Pia Oyarzua, Patricia Bovio-Winkler, Claudia Etchebehere, Maria Eugenia Suarez-Ojeda
Summary: This study evaluated different molecular approaches for studying bacterial communities in an anammox reactor, finding that universal primers had low coverage, functional gene methods provided taxonomic resolution at the species level, and targeted qPCR primers showed consistency in quantification. Recommendations were made to consider genomic database updates and coverage when choosing a biomolecular approach.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2021)
Article
Soil Science
Gerhard Du Preez, Mieke Daneel, Ron De Goede, Marie Joey Du Toit, Howard Ferris, Hendrika Fourie, Stefan Geisen, Thomais Kakouli-Duarte, Gerard Korthals, Sara Sanchez-Moreno, Jan Henrik Schmidt
Summary: The health and functioning of soil ecosystems are vital for sustainable food production and land management. Indices based on nematode community structure are widely used by soil ecologists. This review evaluates the application and future directions of nematode-based indices, providing a framework for selecting indices based on ecological mechanisms for hypothesis testing.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Daniel Vaulot, Stefan Geisen, Frederic Mahe, David Bass
Summary: Metabarcoding of microbial eukaryotes has greatly advanced in the past decade, with the development of a database listing 285 primers and 83 unique primer pairs used for eukaryotic 18S rRNA gene metabarcoding. An R-based web application has been developed to assist researchers in making informed primer choices and including protists in their investigations.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Plant Sciences
Stefan Geisen, Robin Heinen, Elena Andreou, Teun van Lent, Freddy C. ten Hooven, Madhav P. Thakur
Summary: The study found that microbial groups did not affect plant growth and only fungi increased defense compounds in early- and mid-successional forbs. In early successional forbs, shoot biomass-defence relationships were negatively correlated in most microbial treatments, while in mid-successional forbs, they were positively correlated in several microbial treatments. The presence of different microbiomes commonly removed the observed growth-defence relationships.
Article
Ecology
Farzad Aslani, Stefan Geisen, Daliang Ning, Leho Tedersoo, Mohammad Bahram
Summary: Soil fungi, protists, and animals are essential for ecosystem functions in terrestrial ecosystems, but there is still a lack of holistic understanding of the processes shaping the global distribution of the eukaryome. The study found that the community structure of eukaryotic microbes and animals is primarily determined by soil pH and mean annual precipitation, with contrasting latitudinal diversity patterns observed. Additionally, there may be a potential link between body size and niche breadth of soil eukaryotes and the relative effects of ecological processes and environmental factors in driving their biogeographic patterns.
Article
Plant Sciences
Vincent E. J. Jassey, Romain Walcker, Paul Kardol, Stefan Geisen, Thierry Heger, Mariusz Lamentowicz, Samuel Hamard, Enrique Lara
Summary: Soil algae, together with other microorganisms, play a crucial role in the global carbon cycle by fixing atmospheric carbon through photosynthesis. This study compiled a dataset on soil algae and used machine learning modeling to predict their productivity at a global scale. The findings emphasize the significance of soil algae in the global carbon cycle and highlight the need to include their contribution in carbon emission mitigation strategies.
Article
Soil Science
Johan De Gruyter, James T. Weedon, Evelyne M. Elst, Stefan Geisen, Marcel G. A. Van der Heijden, Erik Verbruggen
Summary: The interaction between AM fungi and plants shapes the surrounding soil microbial communities, possibly due to enhanced growth of host plants changing the amount, timing, and form of carbon inputs into soil. This study found changes in the community composition of soil microbial groups in mesocosms inoculated with AM fungi on grass and clover plants, leading to increased plant productivity and other performance measures.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Biodiversity Conservation
Alejandro Berlinches de Gea, Yann Hautier, Stefan Geisen
Summary: Biodiversity, both aboveground and belowground, is negatively affected by global changes such as drought or warming. This article highlights the need to understand the relationship between soil biodiversity and ecosystem functioning under the influence of interactive global change drivers. The results from scarce studies studying interactive effects range from antagonistic to additive to synergistic, indicating the importance of quantitatively accounting for the impacts of interactive global change drivers on soil biodiversity and ecosystem functioning relationships.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Plant Sciences
Chengyuan Tao, Zhe Wang, Shanshan Liu, Nana Lv, Xuhui Deng, Wu Xiong, Zongzhuan Shen, Nan Zhang, Stefan Geisen, Rong Li, Qirong Shen, George A. Kowalchuk
Summary: Host-associated fungi can protect plants from pathogens and their activity can be enhanced by introducing probiotics. However, the mechanisms behind the success of probiotic application are still not well understood, limiting the development of disease control strategies. In a three-season experiment, we found that Trichoderma-amended biofertilizer effectively reduced the incidence of banana Fusarium wilt disease by modifying the fungal microbiome, including reducing the density of Fusarium oxysporum and enriching pathogen-suppressing fungi (Humicola). These changes were accompanied by an expansion in microbial carbon resource utilization potential, contributing to disease suppression. Moreover, the Trichoderma-Humicola consortia demonstrated disease suppression actions, potentially through niche overlap with the pathogen and induction of plant systemic resistance.
Article
Ecology
Alena S. Gsell, Arjen Biere, Wietse de Boer, Irene de Bruijn, Gotz Eichhorn, Thijs Frenken, Stefan Geisen, Henk van Der Jeugd, Kyle Mason-Jones, Annelein Meisner, Madhav P. Thakur, Ellen van Donk, Mark P. Zwart, Dedmer B. Van de Waal
Summary: Parasite performance-response curves are expected to be broader than those of their hosts. However, certain environmental conditions may limit parasite performance more than the host, providing an environmental refuge from disease. Environmental disease refuges respond to global change and not just climate warming.
Article
Biodiversity Conservation
Guixin Li, Rutger A. A. Wilschut, Shuaiwei Luo, Han Chen, Xiangtai Wang, Guozhen Du, Stefan Geisen
Summary: Aboveground, large and higher trophic-level organisms often respond more strongly to environmental changes than small and lower trophic-level organisms. However, whether this trophic or size-dependent sensitivity also applies to the most abundant animals, microscopic soil-borne nematodes, remains largely unknown. Here, we sampled an altitudinal transect across the Tibetan Plateau and applied a community-weighted mean (CWM) approach to test how differences in climatic and edaphic properties affect nematode CWM biomass at the level of community, trophic group and taxon mean biomass within trophic groups. We found that climatic and edaphic properties, particularly soil water-related properties, positively affected nematode CWM biomass, with no overall impact of altitude on nematode CWM biomass. Higher trophic-level omnivorous and predatory nematodes responded more strongly to climatic and edaphic properties, particularly to temperature, soil pH, and soil water content than lower trophic-level bacterivorous and fungivorous nematodes. However, these differences were likely not (only) driven by size, as we did not observe significant interactions between climatic and edaphic properties and mean biomasses within trophic groups. Together, our research implies a stronger, size-independent trophic sensitivity of higher trophic-level nematodes compared with lower trophic-level ones. Therefore, our findings provide new insights into the mechanisms underlying nematode body size structure in alpine grasslands and highlight that traits independent of size need to be found to explain increased sensitivity of higher trophic-level nematodes to climatic and edaphic properties, which might affect soil functioning.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Stefan Geisen, Enrique Lara, Edward Mitchell
Summary: Soil protists are being increasingly studied due to their diversity and importance in ecosystems, but many of these studies lack depth in knowledge and use incorrect terms and interpretations. This paper aims to help non-experts avoid common errors in studying soil protists, providing suggestions for appropriate terms and highlighting challenges in interpreting data. It warns against relying on incomplete reference databases and drawing causal inferences without experimental confirmation and understanding of taxa biology. The authors envision this work to contribute to a better understanding of soil ecology by facilitating the inclusion of protists in ecological analyses.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Plant Sciences
Olivera Topalovic, Stefan Geisen
Summary: Plant-nematode interactions are usually studied from a negative perspective, focusing on plant-parasitic nematodes (PPNs) due to their significant agronomic losses. However, the role of nonparasitic free-living nematodes (FLNs), which outnumber PPNs, in plant performance remains largely unknown. This article provides a comprehensive overview and recent insights into soil nematodes, highlighting the direct and indirect links between PPNs, FLNs, and plant performance. It emphasizes the potential of FLNs as important indirect drivers of plant performance, such as their ability to improve disease suppression in the rhizosphere and stimulate resistance to pests. Overall, this study presents a holistic view of soil nematodes as both positive and negative contributors to plant performance, particularly underscoring the underexplored role of FLNs.
Article
Ecology
Chloe Durot, Miguel Limachi, Kazuya Naoki, Marc Cotter, Natacha Bodenhausen, Luis Marconi, Laura Armengot
Summary: This study compared species richness and community composition of terrestrial ants in six different systems in Bolivia. The results showed that species composition mainly differed between fallow and production systems, and within the latter, it followed the management intensity gradient. These findings highlight the importance of agroforestry systems and natural forests for ant diversity conservation.
BASIC AND APPLIED ECOLOGY
(2023)
Article
Soil Science
Alejandro Berlinches de Gea, Guixin Li, Jingxuan Olivia Chen, Wenjia Wu, Aarzoo Kohra, Semih Karst Aslan, Stefan Geisen
Summary: Biodiversity and ecosystem functioning (BEF) are often positively correlated, but the impact of soil biodiversity on plant performance is still not well understood. This study manipulated microbiome predatory protist diversity to investigate its effect on plant biomass, and found that the relationship between soil biodiversity and plant biomass is context-dependent. Positive soil BEF relationships may not be the norm and should be evaluated in a context-dependent manner.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Microbiology
Daniel J. Wieczynski, Kristin M. Yoshimura, Elizabeth R. Denison, Stefan Geisen, Jennifer M. DeBruyn, A. Jonathan Shaw, David J. Weston, Dale A. Pelletier, Steven W. Wilhelm, Jean P. Gibert
Summary: We provide a roadmap for understanding the impact of viral infections within microbial food webs on ecosystem carbon and nutrient cycling in the context of global warming. Microorganisms play a crucial role in carbon and nutrient cycles and act as a link between ecosystems and climate. However, viral infections within complex microbial food webs pose a significant challenge in predicting and understanding ecosystem responses to warming. We highlight the need for further research on virus-microbe-temperature interactions and their effects on ecosystem functioning in the face of climate change.
FEMS MICROBIOLOGY ECOLOGY
(2023)
Review
Biology
Paula Arribas, Carmelo Andujar, Kristine Bohmann, Jeremy R. DeWaard, Evan P. Economo, Vasco Elbrecht, Stefan Geisen, Marta Goberna, Henrik Krehenwinkel, Vojtech Novotny, Lucie Zinger, Thomas J. Creedy, Emmanouil Meramveliotakis, Victor Noguerales, Isaac Overcast, Helene Morlon, Anna Papadopoulou, Alfried P. Vogler, Brent C. Emerson
Summary: Metazoan metabarcoding is an important strategy for biodiversity inventorying, but differences in workflows might compromise data integration. To address this issue, a modular framework for harmonized data generation was proposed, focusing on terrestrial arthropods. Key points for harmonization were identified and guidelines were provided to reduce methodological options and promote best practice.
